LncATLAS database for subcellular localization of long noncoding RNAs

Abstract

The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

“…To further investigate the distribution of transcripts across the cytosolic and nuclear fractions and identify genes that show differential abundance between nucleus and cytosol, we first investigated how different classes of transcripts are distributed. We found that protein-coding genes were equally distributed between the nuclear and the cytosolic fractions, whereas lncRNAs and small nucleolar RNAs (snoRNAs), as previously shown 29 , were more abundant in the nuclear fraction ( Figure 1C and D). We could confirm the nuclear localization of a number of highly expressed lncRNAs with known nuclear localization (including XIST and MALAT1).…”

Expression profiling of long noncoding RNA identifies lnc‐MMP3‐1 as a prognostic biomarker in external auditory canal squamous cell carcinoma

“…We first found that expression of lnc-MMP3-1 was increased in ESCC tissues compared with EACE by FISH. Our findings were also consistent with those of LncATLAS database [32], which demonstrated cytoplasmic localization of lnc-MMP3-1. For further exploring the clinicopathological roles and prognostic value of lnc-MMP3-1, we divided the EACSCC patients into two groups: high expression group and low expression group.…”

SNPs in LncRNA genes are associated with non‐small cell lung cancer in a Chinese population

“…SNP rs498238 is located in the fourth exon of the long intergenic non‐coding RNA 1833 gene ( LINC01833 ), and the lncRNA, initially named as loc100130502 , is predicted to stay mainly in the nucleus of A549 cells . In the NCBI GEO database, loc100130502 was shown to be upregulated in NSCLC tumors compared to matched adjacent non‐tumor tissues of non‐smoking women in one dataset GSE19804 (Figure A), but no difference in another dataset GSE18842 (Figure B).…”

“…SNP rs3113503 is an intron variant which is located in a gene encoding two long non‐coding transcripts, including a shorter lncRNA named LINC01614 and a longer one called LINC00607 . LINC00607 is present mainly in cell nucleus, and significant downregulation was observed in NSCLC when we analyzed the online datasets GSE19804 (Figure C) and GSE18842 (Figure D). No expression information was found for lnc‐NDUFS6‐5:5 (rs16901995) and loc105369301 (rs219741).…”